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/**
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* Copyright (C) 2009 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.tcsxml;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.common.ResultWrapper;
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import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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/*import eu.etaxonomy.cdm.model.reference.Article;
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import eu.etaxonomy.cdm.model.reference.Book;
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import eu.etaxonomy.cdm.model.reference.BookSection;
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import eu.etaxonomy.cdm.model.reference.Journal;
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import eu.etaxonomy.cdm.model.reference.PersonalCommunication;
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import eu.etaxonomy.cdm.model.reference.PrintSeries;*/
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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//import eu.etaxonomy.cdm.model.reference.WebPage;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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public final class TcsXmlTransformer {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(TcsXmlTransformer.class);
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//TypeDesignation
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public static SpecimenTypeDesignationStatus typeStatusId2TypeStatus (int typeStatusId) throws UnknownCdmTypeException{
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switch (typeStatusId){
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case 1: return SpecimenTypeDesignationStatus.HOLOTYPE();
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case 2: return SpecimenTypeDesignationStatus.LECTOTYPE();
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case 3: return SpecimenTypeDesignationStatus.NEOTYPE();
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case 4: return SpecimenTypeDesignationStatus.EPITYPE();
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case 5: return SpecimenTypeDesignationStatus.ISOLECTOTYPE();
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case 6: return SpecimenTypeDesignationStatus.ISONEOTYPE();
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case 7: return SpecimenTypeDesignationStatus.ISOTYPE();
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case 8: return SpecimenTypeDesignationStatus.PARANEOTYPE();
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case 9: return SpecimenTypeDesignationStatus.PARATYPE();
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case 10: return SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE();
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case 11: return SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE();
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case 12: return SpecimenTypeDesignationStatus.SYNTYPE();
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case 21: return SpecimenTypeDesignationStatus.ICONOTYPE();
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case 22: return SpecimenTypeDesignationStatus.PHOTOTYPE();
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default: {
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throw new UnknownCdmTypeException("Unknown TypeDesignationStatus (id=" + Integer.valueOf(typeStatusId).toString() + ")");
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}
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}
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}
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/** Creates an cdm-Rank by the tcs rank
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*/
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public static Rank rankCode2Rank (String strRank) throws UnknownCdmTypeException{
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if (strRank == null){return null;
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//genus group
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}else if (strRank.equals("infragen")){return Rank.INFRAGENUS();
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}else if (strRank.equals("subgen")){return Rank.SUBGENUS();
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}else if (strRank.equals("gen")){return Rank.GENUS();
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//genus subdivision
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//TODO
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}else if (strRank.equals("aggr")){return Rank.SPECIESAGGREGATE();
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}else if (strRank.equals("taxinfragen")){return Rank.INFRAGENERICTAXON();
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}else if (strRank.equals("subser")){return Rank.SUBSERIES();
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}else if (strRank.equals("ser")){return Rank.SERIES();
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}else if (strRank.equals("subsect")){return Rank.SUBSECTION_BOTANY();
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}else if (strRank.equals("sect")){return Rank.SECTION_BOTANY();
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//species group
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}else if (strRank.equals("subsp_aggr")){return Rank.SUBSPECIFICAGGREGATE();
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}else if (strRank.equals("ssp")){return Rank.SUBSPECIES();
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}else if (strRank.equals("sp")){return Rank.SPECIES();
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//below subspecies
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}else if (strRank.equals("cand")){return Rank.CANDIDATE();
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}else if (strRank.equals("taxinfrasp")){return Rank.INFRASPECIFICTAXON();
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}else if (strRank.equals("fsp")){return Rank.SPECIALFORM();
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}else if (strRank.equals("subsubfm")){return Rank.SUBSUBFORM();
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}else if (strRank.equals("subfm")){return Rank.SUBFORM();
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}else if (strRank.equals("fm")){return Rank.FORM();
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}else if (strRank.equals("subsubvar")){return Rank.SUBSUBVARIETY();
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}else if (strRank.equals("subvar")){return Rank.SUBVARIETY();
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}else if (strRank.equals("var")){return Rank.VARIETY();
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//TODO -> see documentation, Bacteria status
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// }else if (strRank.equals("pv")){return Rank;
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// }else if (strRank.equals("bv")){return Rank.;
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}else if (strRank.equals("infrasp")){return Rank.INFRASPECIES();
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//above superfamily
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}else if (strRank.equals("infraord")){return Rank.INFRAORDER();
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}else if (strRank.equals("ord")){return Rank.ORDER();
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}else if (strRank.equals("superord")){return Rank.SUPERORDER();
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}else if (strRank.equals("infracl")){return Rank.INFRACLASS();
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}else if (strRank.equals("subcl")){return Rank.SUBCLASS();
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}else if (strRank.equals("cl")){return Rank.CLASS();
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}else if (strRank.equals("supercl")){return Rank.SUPERCLASS();
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}else if (strRank.equals("infraphyl_div")){return Rank.INFRAPHYLUM();
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}else if (strRank.equals("subphyl_div")){return Rank.SUBPHYLUM();
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}else if (strRank.equals("phyl_div")){return Rank.PHYLUM();
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}else if (strRank.equals("superphyl_div")){return Rank.SUPERPHYLUM();
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}else if (strRank.equals("infrareg")){return Rank.INFRAKINGDOM();
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}else if (strRank.equals("subreg")){return Rank.SUBKINGDOM();
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}else if (strRank.equals("reg")){return Rank.KINGDOM();
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}else if (strRank.equals("superreg")){return Rank.SUPERKINGDOM();
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}else if (strRank.equals("dom")){return Rank.DOMAIN();
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}else if (strRank.equals("taxsupragen")){return Rank.SUPRAGENERICTAXON();
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//family group
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}else if (strRank.equals("infrafam")){return Rank.FAMILY();
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}else if (strRank.equals("subfam")){return Rank.FAMILY();
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}else if (strRank.equals("fam")){return Rank.FAMILY();
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}else if (strRank.equals("superfam")){return Rank.FAMILY();
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//family subdivision
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}else if (strRank.equals("intratrib")){return Rank.FAMILY();
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}else if (strRank.equals("subtrib")){return Rank.FAMILY();
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}else if (strRank.equals("trib")){return Rank.FAMILY();
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}else if (strRank.equals("supertrib")){return Rank.FAMILY();
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}
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else {
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throw new UnknownCdmTypeException("Unknown Rank " + strRank);
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}
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}
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/** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
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*/
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public static NomenclaturalCode nomCodeString2NomCode (String nomCode) throws UnknownCdmTypeException{
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if (nomCode != null){
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nomCode = nomCode.trim();
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}
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if (nomCode == null){ return null;
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}else if (nomCode.equals("Botanical")){return NomenclaturalCode.ICNAFP;
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}else if (nomCode.equals("Zoological")){return NomenclaturalCode.ICZN;
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}else if (nomCode.equals("Viral")){return NomenclaturalCode.ICVCN;
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}else if (nomCode.equals("Bacteriological")){return NomenclaturalCode.ICNB;
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}else if (nomCode.equals("CultivatedPlant")){return NomenclaturalCode.ICNCP;
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//TODO code Indeterminate
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// }else if (nomCode.equals("Indeterminate")){return NomenclaturalCode.XXX();
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}
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else {
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throw new UnknownCdmTypeException("Unknown Nomenclatural Code " + nomCode);
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}
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}
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public static boolean isReverseRelationshipCategory (String tcsRelationshipCategory){
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String str = tcsRelationshipCategory.replace("http://rs.tdwg.org/ontology/voc/TaxonConcept#", "");
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if ("HasSynonym".equalsIgnoreCase(str)
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|| "IsParentTaxonOf".equalsIgnoreCase(str)
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|| "IsIncludedIn".equalsIgnoreCase(str)
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|| "DoesNotInclude".equalsIgnoreCase(str)
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){
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return true;
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}
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return false;
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}
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/** Creates an cdm-Rank by the tcs rank
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*/
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public static Reference<?> pubTypeStr2PubType (String strPubType) throws UnknownCdmTypeException{
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String tcsRoot = "http://rs.tdwg.org/ontology/voc/PublicationCitation#";
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String tcsBook = tcsRoot + "Book";
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String tcsJournal = tcsRoot + "Journal";
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String tcsWebPage = tcsRoot + "WebPage";
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String tcsCommunication = tcsRoot + "Communication";
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String tcsBookSeries = tcsRoot + "BookSeries";
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String tcsArticle = tcsRoot + "JournalArticle";
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String tcsBookSection = tcsRoot + "BookSection";
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// Artwork An Artwork type publication.
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// AudiovisualMaterial A Audiovisual Material type publication.
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// BookSeries A Book Series type publication.
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// Commentary A Commentary type publication.
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// Communication A Communication type publication.
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// ComputerProgram A Computer Program type publication.
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// ConferenceProceedings A Conference Proceedings type publication.
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// Determination A Determination type publication.
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// EditedBook A Edited Book type publication.
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// Generic A generic publication.
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// Journal A Journal type publication.
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// MagazineArticle A Magazine Article type publication.
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// Map A Map type publication.
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// NewspaperArticle A Newspaper Article type publication.
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// Patent A Patent type publication.
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// Report A Report type publication.
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// SubReference A Sub-Reference type publication.
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// Thesis A Thesis type publication.
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if (strPubType == null){return null;
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}else if (tcsBookSection.equals(strPubType)){return ReferenceFactory.newBookSection();
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}else if (tcsBook.equals(strPubType)){return ReferenceFactory.newBook();
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}else if (tcsArticle.equals(strPubType)){return ReferenceFactory.newArticle();
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}else if (tcsJournal.equals(strPubType)){return ReferenceFactory.newJournal();
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}else if (tcsWebPage.equals(strPubType)){return ReferenceFactory.newWebPage();
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}else if (tcsCommunication.equals(strPubType)){return ReferenceFactory.newPersonalCommunication();
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}else if (tcsBookSeries.equals(strPubType)){return ReferenceFactory.newPrintSeries();
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}
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else {
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throw new UnknownCdmTypeException("Unknown publication type " + strPubType);
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}
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}
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/** Creates an cdm-RelationshipTermBase by the tcsRelationshipCategory
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*/
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public static RelationshipTermBase<?> tcsRelationshipType2Relationship (String tcsRelationshipType, ResultWrapper<Boolean> inverse) throws UnknownCdmTypeException{
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if (tcsRelationshipType == null){ return null;
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//Synonym relationships
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// }else if (tcsRelationshipType.equals("is synonym for")){return SynonymRelationshipType.SYNONYM_OF();
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}else if (tcsRelationshipType.equals("has synonym")){inverse.setValue(true); return SynonymRelationshipType.SYNONYM_OF();
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//Taxon relationships
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}else if (tcsRelationshipType.equals("is child taxon of")){return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();
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}else if (tcsRelationshipType.equals("is parent taxon of")){inverse.setValue(true); return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();
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//concept relationships
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}else if (tcsRelationshipType.equals("does not overlap")){return TaxonRelationshipType.DOES_NOT_OVERLAP();
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}else if (tcsRelationshipType.equals("excludes")){return TaxonRelationshipType.EXCLUDES();
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}else if (tcsRelationshipType.equals("includes")){return TaxonRelationshipType.INCLUDES();
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}else if (tcsRelationshipType.equals("is congruent to")){return TaxonRelationshipType.CONGRUENT_TO();
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}else if (tcsRelationshipType.equals("is not congruent to")){return TaxonRelationshipType.NOT_CONGRUENT_TO();
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}else if (tcsRelationshipType.equals("is not included in")){return TaxonRelationshipType.NOT_INCLUDED_IN();
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}else if (tcsRelationshipType.equals("overlaps")){return TaxonRelationshipType.OVERLAPS();
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//reverse concept relationships
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}else if (tcsRelationshipType.equals("is included in")){inverse.setValue(true); return TaxonRelationshipType.INCLUDES();
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}else if (tcsRelationshipType.equals("does not include")){inverse.setValue(true); return TaxonRelationshipType.NOT_INCLUDED_IN();
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//TODO
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// }else if (tcsRelationshipType.equals("has vernacular")){return TaxonRelationshipType.X;
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// }else if (tcsRelationshipType.equals("is vernacular for")){return TaxonRelationshipType.X;
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// }else if (tcsRelationshipType.equals("is ambiregnal of")){return TaxonRelationshipType.X;
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// }else if (tcsRelationshipType.equals("is hybrid child of")){return TaxonRelationshipType.X;
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// }else if (tcsRelationshipType.equals("is hybrid parent of")){return TaxonRelationshipType.X;
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// }else if (tcsRelationshipType.equals("is male parent of")){return TaxonRelationshipType.X;
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// }else if (tcsRelationshipType.equals("is first parent of")){return TaxonRelationshipType.X;
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// }else if (tcsRelationshipType.equals("is female parent of")){return TaxonRelationshipType.X;
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// }else if (tcsRelationshipType.equals("is second parent of")){return TaxonRelationshipType.X;
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// }else if (tcsRelationshipType.equals("is teleomorph of")){return TaxonRelationshipType.X;
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// }else if (tcsRelationshipType.equals("is anamorph of")){return TaxonRelationshipType.X;
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}else {
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throw new UnknownCdmTypeException("Unknown RelationshipCategory " + tcsRelationshipType);
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}
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}
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/** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
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*/
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public static NomenclaturalStatusType nomStatusString2NomStatus (String nomStatus) throws UnknownCdmTypeException{
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if (nomStatus == null){ return null;
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}else if ("Valid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.VALID();
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}else if ("Alternative".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
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}else if ("nom. altern.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
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}else if ("Ambiguous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.AMBIGUOUS();
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}else if ("Doubtful".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.DOUBTFUL();
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}else if ("Confusum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONFUSUM();
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}else if ("Illegitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
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}else if ("nom. illeg.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
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}else if ("Superfluous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
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}else if ("nom. superfl.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
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}else if ("Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
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}else if ("nom. rej.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
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}else if ("Utique Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED();
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}else if ("Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED_PROP();
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}else if ("Orthography Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP();
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}else if ("Legitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.LEGITIMATE();
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}else if ("Novum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
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}else if ("nom. nov.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
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292
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}else if ("Utique Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED_PROP();
|
|
293
|
|
|
294
|
}else if ("Orthography Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED();
|
|
295
|
|
|
296
|
}else if ("Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED_PROP();
|
|
297
|
|
|
298
|
}else if ("Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
|
|
299
|
}else if ("nom. cons.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
|
|
300
|
|
|
301
|
}else if ("Sanctioned".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SANCTIONED();
|
|
302
|
|
|
303
|
}else if ("Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
|
|
304
|
}else if ("nom. inval.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
|
|
305
|
|
|
306
|
}else if ("Nudum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
|
|
307
|
}else if ("nom. nud.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
|
|
308
|
|
|
309
|
}else if ("Combination Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.COMBINATION_INVALID();
|
|
310
|
|
|
311
|
}else if ("Provisional".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
|
|
312
|
}else if ("nom. provis.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
|
|
313
|
}
|
|
314
|
else {
|
|
315
|
throw new UnknownCdmTypeException("Unknown Nomenclatural status type " + nomStatus);
|
|
316
|
}
|
|
317
|
}
|
|
318
|
|
|
319
|
|
|
320
|
}
|